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Chapter 2
General Chemistry
Carbon Compounds
Enzymes
General Chemistry
• Atoms
– Basic unit of matter
– Made up of a dense core called the nucleus
(protons and neutrons) surrounded by
electrons
Elements and Isotopes
• Elements are pure substances that consist
of only one type of atom
• Isotopes are atoms of an element that
have the same number of protons, but a
different number of neutrons
• Why do we care as biologists? They
make very good identification markers for
certain biological molecules like proteins
and DNA
Chemical Compounds
• Elements can be combined in definite
proportions to form compounds
– CO2, H2O, C6H12O6, NaCl
– The smallest unit of any compound is called a
molecule
Chemical Bonds
• Valence (outside) electrons determine the
type of bond that will form
• An atom always wants to have 8 valance
electrons
Yahoo! Video Detail for 02-12CovalentBonds.mov
• Covalent Bonds
– Electrons are shared between atoms
– Very strong bond
– A single covalent bond (2 electrons are
shared) is shown by a single line between
atoms
C-C
– A double bond (4 electrons are shared) is
shown as two lines
C=C
• Ionic Bonds
– One atom gives up an electron or electrons to
another atom
– Not as strong as a covalent bond
– Atoms that gain or lose electrons are called
ions.
NaCl  Na+ and ClMovies from lecture May 26
Water
• We are 85% Water. It is so important to
us because it is polar
– Polar means it has a slightly positive side and
a slightly negative side
• The polarity of water is so important to us
because this is what makes water such a
good solvent.
– Ionic compounds like NaCl can be easily
dissolved in water.
Hydrogen Bonds
• Very important to biological systems
• Holds water molecules together and DNA
molecules
– The slightly negative end of one molecule is
attracted to the slightly positive hydrogen
atom on another molecule
– A bond strong enough to hold molecules
together, but not so much that they can’t be
separated easily.
Solutions
• Solutions consist of a solvent (the substance
that does the dissolving) and a solute (the
substance that is dissolved)
Name the solvent and the solute in the following
example:
Sea Water
Water = Solvent
Salt = Solute
Acids and Bases
When water separates…
H2O  H+ + OH• If the concentration of H+ is higher than
water, the solution is an acid
• If the concentration of H+ is lower than
water the solution is a base
pH Scale
• pH 7 = Neutral (pure water)
• pH < 7 = Acid
• pH > 7 = Base
Buffers
• Binds with H+ ions when concentration is
too high (too acidic)
• Releases H+ ions when concentration is
too low (too basic)
• Prevents sharp changes in pH in biological
systems
• Ex. Blood bicarbonate buffer system
• CO2 + H2O  H2CO3  HCO3- + H+
– When too much CO2 builds up in the blood
(acidic), more HCO3- is produced
This system works with the kidneys which
eliminate the HCO3- (a base) when the pH is
too high (part of the excretory system)
Don’t forget this is all part of Homeostasis!!!
Organic Compounds
• Organic compounds are carbon
compounds that make up living things or
that come from living things.
• The four elements that make up 99% of all
living things are: C, H, O, N, P
Biomacromolecules
• Bio = life
• Macro = big
• Biomacromolecules = big molecules that
make up life
• There are four classes of
biomacromolecules
Biomacromolecules are Polymers
• Poly = many
• Meric = units
– A polymer is made up of many units
• A monomer is the subunit of any polymer
– A polymer is made up of many monomers
Carbohydrates
• Made up of the elements C, H, O in a
1:2:1 ratio
– Example: Glucose C6H12O6
• The most important function of
carbohydrates is energy storage
• Another important function is building
material for plants, fungi and bacterial cell
walls
Carbohydrates = Sugar
• Saccharide = sugar
• Mono = one
– Monosaccharide = one
sugar
– Examples: Glucose,
fructose, galactose
– Quick, easy energy
• Disaccharide = two sugars
• Examples: lactose, maltose, sucrose
• Also quick, easy energy
Polysaccharides
• Polysaccharides = many sugars
• Long lasting energy storage
• Building materials for plants
Starch
• Polymer made up of glucose monomers
• Energy storage molecule of plants
Cellulose
• Polymer made up of
glucose monomers
• Building material of
plants
• Cannot be digested
by humans
• Cows have a stomach
that contains rumen
to digest cellulose
Glycogen
• Polymer made up of glucose subunits
• Energy storage molecule of animals
– Found in liver and muscle cells
– Gives quick burst of energy for fight or flight
mode
Glycogen gives us that quick burst of energy for fight or flight
Lipids
• Primary function is energy storage
• Also makes up cell membranes, waxes,
steroids
• Contains the elements C,H,O
Lipids are Hydrophobic
Hydro = water
Phobic = fear
Hydrophobic = afraid of water
Hydrophobic = non polar
Think of Italian salad dressing or a freshly
waxed car
Fats are lipids
• Fats are for energy
storage
• Gram for gram, they
provide more energy
than carbohydrates
• Fats often have a
polar (water soluble)
head and non polar,
fatty acid tails
– There are three main
types of fatty acid tails
• Saturated Fats
– Have C-C single bonds, straight tails, and are
“saturated” with hydrogen atoms.
– Solid at room temperature
– Examples include: Butter, Animal fat
– Can contribute to heart disease because they
raise levels of cholesterol in the blood
• Unsaturated Fats
– Have C=C double bonds that are
“unsaturated” with hydrogen atoms
– Liquid at room temperature
– Tails have “kinked chains”
– Oils
• Trans fats
– A hydrogenated fat used in
the manufacture of
margarine and snack foods.
– We can’t digest large
amounts of trans fats so
they become incorporated
into our cell membranes
which prevents them from
functioning properly
Butter vs. Margarine
• Butter is high in both saturated fat and
cholesterol which contribute to heart
disease
• Hard, butter-like margarines contain high
amounts of trans fats which are also
unhealthy.
• Soft margarines contain the least amount
of harmful fats and are high in unsaturated
plant fats
Nucleic Acids
• Class of Biomacromolecules that includes
DNA and RNA
– The monomer is the nucleotide
– Contains the elements C,H,O,N,P
– The function of a nucleic acid is to store and
transmit genetic information
• The nucleotide consists of three parts:
– phosphate group
– five carbon sugar
– nitrogenous base
• The difference between DNA and RNA
– DNA has the sugar Deoxyribose
– RNA contains the sugar Ribose
– DNA is double stranded
– RNA is single stranded
Proteins
• Class of Biomacromolecules that contains
the elements C,H,O,N
• Proteins are polymers
• Monomer of proteins are amino acids
• Proteins are sometimes called
polypeptides because amino acids are
held together by peptide bonds
Peptide bonds
• Peptide bonds are
formed by
dehydration/synthesis
reactions
– Dehydration means
that water is removed
during the bond
formation
What do proteins do?
• Proteins have many important functions
• Their shape determines the function of the
protein
• The shape is determined by the “R”
groups that are part of each amino acid
So, what do proteins do?
• Some have important structural roles
– Skin, hair, nails, muscle tissue, connective
tissue, bones and skin are all made up of
protein
• Another very important role of proteins is
the enzyme
– A biological catalyst
• A catalyst speeds up chemical reactions
Enzymes are very specific
• Enzymes have a very specific area (active
site) that binds to the reactants of the
chemical reaction (substrates)
• Nothing else can bind and work the same
Enzymes are Sensitive
• Heat and pH changes can affect the
activity of an enzyme
• Remember shape determines function, if
we change the shape of the protein, it
won’t work anymore
Enzymes are Sensitive
• pH changes can change shape of protein
altering function of enzyme
• Heat can cause the enzyme to fall apart
(denature)
• Cold causes the enzyme to function more
slowly
• Mutations in the DNA can change the
shape and function of an enzyme
Enzymes in the human body have an optimum
temperature of around 37º C, enzymes from
plants and invertebrates may have lower optimum
temperatures. Some bacteria living in hot springs
have enzymes with much higher optimum
temperatures
Enzyme Graphs
Some things to remember about
enzymes…
• When more substrate is added, enzymes can
produce more product until a plateau is reached
• When more enzyme is added, more product can
be formed
• Enzymes are reusable